Shadow: The Alternative Story
by Blackace70
Summary: My take on what should've happened after the events of SA2. What if when Shadow had fallen to earth after defeating the Bio-Hazard with Sonic, he was found by someone else before Dr. Eggman. Watch as Shadow takes a whole new different path as he fights to learn about his past. And this time...he WILL get his answers. OCs included, Pairings...you'll have to wait and see
1. Chapter 1

_**Hey Ace here with a new story, this one was inspired by a lot of logics and what-if scenarios that appeared in my mind. This is a scenario of what if; when Shadow had fallen down to earth after the events of defeating the Bio-hazard along with Sonic someone else had found him other than Dr. Eggman. This story will pick-up right after Sonic Adventure 2 and go on from there, it will mostly be Shadow centric but Sonic will have a part in this to so rejoice, Sonic fans, the blue hedgehog has a major part in this story. OCs will appear in the fanfic helping Shadow deal with his mysterious past and then forward.**_

_**This story is inspired by logic thinking, and ClementJ642 opinions (The man is a totally hilarious Youtube gamer by the way.) totally fan-based on what I feel (And I'm sure others would agree with me) should have happened when Sega Team decided to bring Shadow back along with a few tweaks. Anyone who reads and likes the story are welcome to give their ideas, I'm always open to suggestion.**_

_**This chapter is more of a mini prologue, the story will pick up on chapter two. Other than that I hope you enjoy.**_

_**Disclaimer: I do not own Sonic or any of its characters, just the OCs that appear in this story**_

Chapter 1: Lost then Found

"_**Shadow…I beg of you…give them a chance to be happy."**_

_That was the only sentence coursing through my mind as I headed towards the falling colony. Looking at the gigantic space laboratory with new found strength and determination I increased my speed towards my target._

"_No way is that getting through." I heard Sonic state "Now Shadow"_

_Steeling myself I raised my hands along with Sonic towards the falling colony and we both shouted at once_

"_CHAOS CONTROL"_

_We engulfed the ark in an orb of light, stopping it in its tracks before teleporting it back into its normal orbit. We had done it, The Ark was stopped, The Bio-lizard was defeated; it was over. The earth was saved._

-X-

Sonic gasped for air trying to catch his breath, using chaos control had taken a lot of him. He could feel his super powers slowly slipping away from him. He turned to head back to the Ark when he paused and went wide eye

"Shadow…" he whispered

He whipped his head around frantically trying to locate the red streaked hedgehog; and when he found him, he got a huge hitch in his breath. Off in the distance was Shadow lying motionless as he drifted away from the Ark and towards Earth; Sonic flew towards him at high speed all the while burning the last of his super energy trying to catch up with him

"SHADOW!" he screamed as he grabbed his arm, the unconscious hedgehog slowly opened his eyes and looked at the worried golden hedgehog

"S-Sonic…"

"Shadow, don't talk, save your strength man. I'm gonna get you to Ark, just hold-"

"Listen…"

Sonic paused in his talking and looked at the ebony hedgehog "You have to leave me behind and get back to the Ark."

"WHAT! No Shadow I can save you, I can-"

"You won't have the energy to make it back Sonic; you'd barely have enough energy to support yourself getting back, much less carrying me." As if to prove Shadow's point both hedgehog's golden fur started to fade back to their original colors signaling that their super forms was starting to wear off "I can pass the last of my Chaos Energy onto you, so that way…at least you'll be able to make it back."

"But…what about you" Sonic gritted, upset by the suggested plan "You could live, finally have the life Maria would've wanted for you."

Shadow let out a smiled, a true genuine smile since his reawakening "Maria always wanted me to make the people of earth be happy. I'm content knowing that her wish is fulfilled and that they'll always get a chance to be happy now that this crisis thanks to the professor has been resolved."

"Shadow…"

Sonic despite himself loosened his gripped a little and felt Shadow to slip between his grasp. Sonic holding onto Shadow by his wrist looked at the slowly reverting hedgehog passing on the last of his Chaos energy to Sonic.

All the while this was happening Shadow had his head lowered all the while still having his smile on his face "Sonic even though we were enemies in the beginning, even though we only teamed up for a short while. You were the closest person I could ever call a friend."

He looked up with happy yet sorrowful expression "Thank you, and…goodbye."

Freeing his wrist from Sonic's grip, the ebony hedgehog started to fall into Earth's orbit gradually becoming a fireball in the process. Sonic could only watch his once enemy now fully atoned hedgehog rival disappear from his sight and towards the earth orbit below. Sonic balled up his fist in anger, up to the point of where his knuckles whitened. He eased up when he felt something his right hand; opening up his palm Sonic made a silent gasp as to what he was holding.

It was Shadow's inhibitor ring, the only sole remnant of the ebony red streaked hedgehog. Sonic wordlessly took off his glove and place the ring on his wrist before placing the glove back on. Flying back to the Ark only on thought remained in Sonic's head

'_I promise Shadow, I will make sure yours and Maria's wish stays a reality. I swear'_

_**-Three Weeks have passed since that day-**_

"God, these robots are starting to get annoying."

Skating through a forest at top speed a young adolescent boy who looked to be at the age of 12; he had long pure black spiky hair that formed a bang with a blue trim on the edges covering his left eye and partially his face and a spiky blue streaked ponytail in the back (Imagine Madara's hairstyle from Naruto in a ponytail.) His outfit consisted of a sleeveless slight hugging deep blue shirt with black panels on the side, black jeans with a sapphire blue flame design at the bottom, white belt with a double row of studded spikes, white sneakers with an black 'X' strap. He was wearing pure white padded gloves that had studded spikes that covered his fingers to the back of his hand and Crimson blood red belt straps wrapped around his forearms. _**VANITY**_

Immediately stopping on a dime the boy came onto three orange robots that had blue eyes sporting a very weird looking smile (In his opinion). Sighing for what could've been the fiftieth time today, Vanity brought his hand up and appearing from under the straps was a red & black two pronged slash harken. The poor unsuspecting robot was mercilessly cleaved in two as the boy fired his harken at the middle of its torso. Seeing the harken wedge itself into the tree behind the robot the young adolescent used that momentum to reel himself in towards the other robots and brought out his second slash harken though instead of it being red, it was blue this time. Instead of firing it Vanity used as a makeshift wrist blade and sliced the robot effectively destroying it. The third grunt bot seeing its first two comrades go down and the person responsible for all that aim its machine gun that it's been carrying for a while and unleashed a hail of bullets towards the young boy though it proved futile as Vanity brought his arm up as if shielding his face and a dark red diamond like shape shield appeared deflecting all the bullets; Vanity kept the shield up until the robot emptied all its clip on the boy. Seeing it was out of ammo the robot looked up to see Vanity appearing in front of it before its head got decapitated by Vanity's slash harken.

Seeing the three robots thoroughly destroyed Vanity started walking "This is the third group of robots I've seen in the last hour. It's starting to get really annoying."

It had been three weeks since the incident with that insane scientist who had threatened and attempted to destroy the earth had been prevented. Sonic, the blue hedgehog that had been falsely accused committing crimes had managed to save them all from a devastating fate. How ironic, that the very people that accused and attempted at condemning him to life in prison ended up being save by that very same hedgehog. Some would call that Fate's very cruel idea of a joke. After the whole ordeal was done these strange robots started to appear out of nowhere; and while Vanity paid no mind to them at first when they started shooting near his house… oh no, no, no, no, no that's when they had to go.

Reaching his house though Vanity couldn't help but wonder why they kept appearing. Were they actually searching for something? If so, then why were they focusing around where he lived? His thoughts were cut off by the sounds of rustling coming from a few bushes near him, no normally that didn't bother Vanity as he would normally chalk that off as an animal. What did grab his attention was the low moan that emitted from same bushes. Slash harken at the ready, Vanity dropped into a defensive stance as a shadowy figure came out of the bushes. Vanity's apprehensiveness turned to shock at what he saw.

As the figure dropped to the ground, only three words could be uttered out of his mouth "Oh…my…God"

End of Chapter

_**Well…chapter one up and running, let see how it goes. As I said before, this is more of a prologue than a real chapter so that's why there wasn't much going on; the action will slowly but surely pick up in chapter two.**_

_**So the reason I was inspired to write was from what I took what ClementJ642 had said on Youtube that got me thinking, along with discussions me and my friend had -who is a diehard Sonic fan like I am by the way- it got me thinking. Sega, after Sonic Heroes, fucked up big time with the franchise and royally decimated Shadow's image with his game. All because Sega had to give into popular demands of the people, instead of using their common sense of how they should go about dealing with Shadow.**_

_**Clement made some pretty good arguments and points about how things had gone when Shadow had been resurrected while he was playing Shadow the Hedgehog; all the while bashing the shit out of that game. And while I normally don't bother with other people's opinions, his seemed really interesting to listen to. Now I not gonna put him on the spot so that you guys who don't agree with me can find him and bash his channel or anything. I'm just saying that I agree with a few things he said and made my own theories of what should've happened.**_

_**Now while this story is going to go on what I felt should have been canon, it's not going to remain canon. Meaning at some point into the story is going to crossover with another universe, but don't worry…that's not gonna been for a long time. So…I think that about covers everything I wanted to talk about, if I forgot something I bring it up next chapter. So anyways I hope you all enjoyed the chapter**_

_**See you next time ^_^**_


	2. Chapter 2

Chapter 2: Time-Skip

_He didn't know how long he had been walking. Nor did he know where he was going. Just soon after waking up to what looked to be like a dense forest, his body started moving on its own. His body screamed pain but his mind wouldn't listen, just setting itself to auto as it kept moving. He finally reached his breaking point as his leg gave out and collapsed under him; his well beyond strained leg muscles pounding with agony. He looked around with a gaze slowly becoming hazy, seeing a pair of legs appearing in his line of sight was the last thing he saw before blacking out and hearing someone calling out to him_

_-Two Months have passed since the Incident -_

Running through the rocky plains at top speed, our blue hero Sonic the hedgehog was zooming through the rocky foundation. His mood throughout the entire run was anything but cheerful, in fact it was the complete opposite; his usual trademark grin that brimmed with his cheeky cocky attitude and confidence was now an impassive straight line that borderline to a frown. His emerald green eyes that were filled with fun and cheeriness were now burning with a type of fierce seriousness you wouldn't expect to see on our lovable blue hedgehog. The reason for this change was due to the mini anniversary.

It had been a little over two months since that incident aboard the Ark, and Sonic had decided to take his duty in battling against Eggman a lot more seriously. That battle against that Bio-Lizard really changed his perspective on life and made him realized that just how life can been easily brought into this world, it can be just as easily taken out of it as well. Sighing, Sonic turned his gaze towards the clear blue sky above him; staring at the endless see of blue above him, his frown deepened ever slightly.

It had also been two months since he had last seen Tails and the others

_Flashback:_

_After reaching the entrance to the Ark safe and sound, Sonic walked back towards the control room in a snail pace. His eyes were blank as he tried to comprehend what had just happened. He was so lost in his thought he failed to realize that he walked right into the middle of the room where everyone gathered around him. Tails bounced happily towards his brother figure_

"_Sonic you did it, you and Shadow saved everyone." The fox exclaimed happily before noticing his surrogate brother's mood "Uh Sonic, What's wrong?"_

_Sonic didn't respond but instead kept his gaze towards the ground_

_Rouge tore her gaze from Sonic and looked around the room realizing that something was off "Sonic…where is Shadow?"_

_That question got a response but not one that she or the others were expecting. Sonic started to ball up his fist, to the point where his knuckles started cracking due to the pressure. Gritting his teeth, he uttered out only one word in a harsh whisper_

"_Gone"_

_Rouge and the other looked confused on what Sonic had meant "Gone, I-I don't understand what do you mean gone?"_

_Something snapped within Sonic, unable to keep his emotions back any longer "Gone Rouge, he's gone! SHADOW SACRIFICED HIMSELF TO SAVE ME, TO SAVE ALL OF US!"_

_Everyone including Eggman was taken aback by Sonic's outburst Tails, being the first to recover, tried to calm his friend "Sonic, I'm sure you've done everything you could…"_

"_No I didn't!" Sonic cut off with a surprised snarl coming out of him, this caused his younger surrogate brother to jump back slightly "Shadow gave up the last of his energy to me, knowing full well he wasn't gonna make it."_

_Sonic dropped towards his knees "And I couldn't do anything to stop him." He started punching the ground "No, more like I __**DIDN'T **__do anything to stop him."_

"_SHADOW GAVE HIS LIFE FOR ME AND I JUST STOOD THERE AND DID NOTHING!"_

_Flashback End_

Sonic gritted his teeth as he unconsciously started boosting up his top speed. He had not meant to go off on Tails and Rouge like that, he honestly didn't, but he had been so frustrated…so angry at what happened, he vented out all of his anger on them at the time. A sudden sound of turbines filled the silent air causing Sonic to break out of his chain of thought.

Looking up he set his sights towards a familiar blue colored plane, currently transformed into its second state. Despite his new mood change Sonic let out a smile at the sight of the familiar plane. The air vehicle started to descend to Sonic's level, revealing two of Sonic's closest friends

"Tails, Knuckles, long time no see." The hedgehog greeted warmly "What've you guys been up to lately?"

"No much for me, I've been in my lab lately, tinkering around with some gadgets I've been building recently." The yellow fox responded looking down towards Sonic

"After our last adventure, I returned back to Angel Island and resumed my duties as a guardian for the Master Emerald." Knuckles stated lounging sideways on the plane

Sonic grinned, turning his attention right back towards the road "What about you Sonic?" Knuckle said suddenly "You still going out searching for-"

"Knuckles" Tails cut off

"What, it's just an honest-"

"Yes" Sonic responded suddenly cutting off any retort Knuckles was about to say for his defense "I have"

Knuckles and Tails didn't say anything, but gave their friend a look of concern. Along with taking his battle with Eggman seriously Sonic had also been searching for Shadow on the side. He was going on the hope that maybe, just maybe Shadow had somehow survived; Sonic knew the chances in finding Shadow would be slim to none, but he had to try. If he could cheat death by teleporting out of a capsule jettisoned to earth using a fake chaos emerald, surely Shadow could survive a fall towards earth. He was the ultimate life form as he proclaimed before, something like this should be nothing to him.

Tails and Knuckles, when they had learned what Sonic had been doing in his spare time, grew worried about their friend. After learning about what happened to Shadow, his death obviously affected everyone; even Dr. Eggman uttered a few prayers and properly mourned for Shadow for a period of time. Out of all of them Sonic took it the worse, no one could blame him though, he did after all watch the hedgehog fall to his doom, helpless to do anything to stop it. But despite that Sonic refused to believe that Shadow was dead; the two honestly didn't know how Sonic came to the conclusion that Shadow was still alive, but they hoped he would snap out of it soon. Sonic didn't realize it but he was letting this whole grief and denial consume, if it didn't end, who knows what could happened.

"I see…" Tails mused quietly "Sonic don't you think you should give up on searching for Shadow?" The young fox flinched when he saw Sonic's piercing glare aimed at him but regardless continued "I'm just saying…it's been two months and you've come up unsuccessful with anything."

Sonic didn't say anything but kept his gaze straight forward

"The way things seem; there might not even be a body to be found." Sonic tensed at that sentence "Depending on where he landed he could have probably been buried under all the natural landscaping. Besides even if you did find him, there's a chance he might not be-"

"What Tails?" Sonic interrupted harshly, his emerald green eyes hardening in anger "Might not be what?"

The young fox once again flinched under his brother's tone of voice, he really wished he had not said anything right now "Might…not be…around with us."

"Sonic" Knuckles called out gaining the hedgehog's attention "I understand how you must be feeling right now, but you've got to slow down with all of this. You've been running yourself ragged these past two months and soon it'll start to take its toll on you. I know all this because; I've been monitoring what you've been doing through the Master Emerald. Sonic…if there is a chance Shadow is still alive we'll find him, but don't push yourself past your limit over this."

Sonic stared long at both of his friends before sighing "You're right, I'm sorry guys I guess I really have been getting carried away." He said with a truly genuine smile, the first smile he's given in two months "So anyway, on a lighter note, what's up?"

"Oh yeah" Tails started digging through the compartment of the Tornado "Sonic, you might want to check this out."

Pulling out a paper he stretched out his arm so that Sonic could grab it. The blue hedgehog jumped snatching the paper and then started running backwards so that he read the paper properly. Upon seeing who was from Sonic immediately grew angry.

"Eggman" he muttered darkly

The letter read as followed:

_Greeting dear Sonic and Co,_

_I the brilliant Dr. Eggman have finally created_

_The ultimate weapon at my disposal, in three_

_Days I will conquer the world, I you wished to _

_Stop me then I offer this challenge up to you, think_

_You beat me within 72 hours?_

_-Dr. Ivo 'Eggman' Robotnik_

"_Well I see his arrogance hasn't diminished within the last two months." _Sonic thought bitterly before smirking "Well it seems to me that Eggman has invited us to party."

He looked up at his two friends "Whaddya say, you two up for another adventure?"

Seeing a piece of their friend coming back, the two grinned before jumping out of the plane and running after their friend (Not before Tail made sure to put the plane on auto-pilot mind you). The trio ran out of the rocky plains, ready to take on whatever what was in store for them.

-X-

"_Shadow what do you think it's like on earth?"_

"_The professor said his life's work was dedicated to all of those who live down there. He once told that the reason for his existence was making people happy through the power of science."_

_The blonde looked at the hedgehog after giving his answer with slight concern "Shadow…"_

"_Maria, I just don't know anything anymore. I often wonder why I was created. What my purpose is for being here. Maybe if I go down there, I will find the answers. Maybe…"_

_The hedgehog now known as Shadow went up to the window and put his hand on the glass_

"_Maria…"_

…_Shadow….Shadow…_

_ -X-_

"SHADOW"

The ebony hedgehog that had been deep in thought was brought out of his reverie due to violent shaken through his shoulder. Shadow looked to see Vanity looking concerned "Shadow are you alright, you blanked out again."

"Huh, y-yeah I just…"

"You had another memory burst, didn't you?"

Shadow looked at Vanity, who bore the expression of that he had been right in his assumption. If Shadow was surprised by how easily he figured him out, he wasn't showing it; then again, there was no reason to ever since he had started living with Vanity.

When Shadow had appeared near Vanity's house on the borderline between life and death, Vanity immediately took him in and treated back to health. During the time Shadow was under Vanity's care he had come to the realization that he had lost his memories when he could not remember anything after Vanity had asked where he was from. The black hedgehog tried hard but could remember anything. The only reason he even knew his name was thanks to Vanity, who -having the ability to scan someone's mind- was able to search through Shadow's shattered memory banks and successfully salvage it; surprisingly to Vanity as well, the boy had also found memories of Shadow's fighting capabilities as well as his chaos abilities intact. Vanity had made sure to salvage that as well just in case if it would come in handy in the future.

Since that day Shadow had decided to remain with Vanity; not just because he didn't where he lived (If he lived anywhere at all) but so that Vanity could keep an eye on Shadow and help him with his memories in case they came back little by little.

Shadow looked back towards the ocean, staring at the deep blue sea "Yeah, this time it was a memory of me and a blonde haired girl. I don't really have much about her except for her name."

"Which is?"

"Maria…"

Vanity put a finger over his lip musing in thought, he noticed that recently Shadow's memory pieces have been coming in swarms; so frequently that he had dubbed these visions 'memory bursts'. If he was going to be honest with anyone, he hated it when his brother got like this. Yes brother, in the two months Shadow had been living with him the two had grown close where Vanity had started to see Shadow as like an older brother. The same could be said for the ebony furred hedgehog, as he grew close to Vanity as well. They even started to grow the habit of calling each other brothers every once and a while.

Putting a hand on Shadow's shoulder Vanity gave a comforting grin "Well…we'll examine the memory when we get back. But for let's get going, you said you wanted to see the Ocean Palace right; it's not far from here."

Shadow smirk before racing off with Vanity towards the edge of the beach, until they had reached a large white and red stone city like fortress. Ocean Palace, as the name implies, is a large fortress city that has lots of pathways that runs along, through and even under the ocean. It had been rumored by many people that the palace was a part of the fabled City of Atlantis. Ocean Palace is not only a historical sight to behold; it was also quite a tourist attraction that was generally opened to the public, though some boundaries were set as to prevent people from entering dangerous areas.

As they walked through the ancient like city, Shadow and Vanity were awestruck by the foundation of the area. The place seemed to have been over centuries old, yet the city looked as if it was brand new; truly it was a sight to behold

"Honestly" Vanity began "Its things like this that makes you appreciate the many wonders the world has to offer you."

Shadow nodded as looked around the whole area, everything about the place was just incredible; from the smooth stone texture, the beautiful carvings along the pathway and walls, as well as the fairly large missile speeding towards the city a high velocity.

….Wait….

"Missile" Shadow whispered in a silent alarmed as he watched the incoming warhead fly and into one of the high parts the of the palace before he could even say anything

A huge explosion occurred followed by a violent shock vibration, surprising all of the patrons who were visiting Ocean Palace. Many screamed in alarm and fear as they fell to the ground due to the ancient city shaking, Vanity, unceremoniously fell on his butt while Shadow –who had seen the warhead coming- dropped to one knee.

Slowly steadying himself as he got up, Vanity started rubbing his bruised ass as he glared towards the sky "What the hell was that?!" he demanded, his tone laced with shock, anger, confusion, and surprise

Shadow kept his gaze glued towards the ocean; the next sight he saw made him pale. Several more missiles were charging towards the palace, each of them varying in different sizes.

"Oh no"

-X-

Watching the missile explosions with a mildly impassive look on his face was a fairly age man and well known and feared genius. He watched on as explosion occurred followed by the people running around fearing for their lives and the lives of their loved ones. An army of robotic drones surrounded him all bearing a certain familiar smile on their faces.

"Search for the Chaos Emerald." Was the man's only order "Level the whole city if you must."

End of Chapter

_**Here's the second chapter of the story and things starts to pick up. Again there's not a lot of action but I'm trying to make this flow at a steady pace, the action will come soon have no worry about that. **_

_**Also I hope some of you don't have a problem on with how I portrayed Sonic in this chapter; I have no intention of making him some kind of negative, angst type of person. When the aftermath of the Bio-Hazard changed him, it changed him A LOT; don't worry Sonic will return to his cheery, fun-loving self soon enough.**_

_**As always, I hoped you all enjoyed this chapter**_

_**See you next time ^.^**_


End file.
